The minister, Jean Andre Soja, said a government assessment also found 32,000 hectares of rice fields, the staple food, completely flooded.

The flooding, which spanned the northwest and eastern coastal regions of the giant Indian Ocean island, worsened last week when the eastern lake Alaotra burst its banks, engulfing villages and crops, Soja said.

"There are villages around lake Alaotra completely under water," Soja said at a press conference. "The emergency for us is to find temporary homes for thousands of people and to provide food and medicine."

Soja said water sterilising kits were being distributed in the affected regions to prevent the spread of water borne diseases.

"There is a serious risk of an epidemic," he added.

He said several roads in the region were also mostly flooded, hampering access for relief efforts.

Aid agencies have raised concerns about the long-term impact of the floods on the country's food supply. Some of the worst affected regions are among the island's most agriculturally productive.

"These crops were almost ready to be harvested, then these flash floods come, so they're all ruined," said Maherisoa Rakotomirainy, an analyst at the UN World Food Programme.

Each hectare of rice fields destroyed is a loss of about 1-2 tonnes of rice, officials said. Madagascar's 17 million people consume almost 2.5 million tonnes annually, making it one of the biggest per-capita consumers of rice in the world.

The island suffered severe rice shortages last year when cyclones Elita and Gafilo tore up crops in January and March, sparking major street protests as prices rocketed.

But Rakotomirainy said the likely impact of the floods would not be as devastating as last year's cyclones.